there are a couple of HUGE issues with "cover systems". first and the most important is that they are essentially a cheat if done in third person mod. you can see up and over the containers or around corners while the npcs cannot. games are easy enough as it is i dont need anymore help thank you. the second one is that they have to justify having all sorts of waste high objects randomly scattered around the game world. when i was playing ME2 i kept thinking that all the dock workers were on strike or something cause there were always tons of crates just lying around at odd angles. in the end it makes the game world look incredibly stupid.
the best ive seen (havent played Crysis 2 yet so i cant comment on that) is the one they are putting in red orchestra 2. you essentially hug whatever your hiding behind BUT you can only see beyond it if you poke your head over and risk getting shot. you can also blind fire in that game which is kind of neat. i do agree with the wall hugging in the thief games though. that was kind of nifty even though i personally rarely used it.
i cant wait for this fad to go away and i think its more of a "run n gun" gameplay mechanic than a "swords n boards".